| c6c3460 | Ronny Lorenz | 14 November 2016, 18:28:53 UTC | Bump to version 2.3.1 | 15 November 2016, 10:01:19 UTC |
| b7d4f03 | Ronny Lorenz | 15 November 2016, 09:46:38 UTC | Expose more data fields in SWIG interface(s) for several data structures - Almost all data fields for vrna_md_t, vrna_param_t, and vrna_exp_param_t are directly accessible from scripting languages now | 15 November 2016, 09:50:39 UTC |
| 409f121 | Ronny Lorenz | 14 November 2016, 18:24:58 UTC | Fix SWIG wrapper for 'subopt' functions and methods - Return values of this overloaded method are freed automatically, so we must not declare them 'newobject'. Otherwise, double free corruption might occur - Ensure the uniq_ML switch is active before filling MFE matrices for subopt - Add separate unit test suite for SWIG wrapped subopt functions/methods | 15 November 2016, 09:49:27 UTC |
| 1f90700 | Ronny Lorenz | 14 November 2016, 17:35:23 UTC | Fix several issues in SWIG interface(s) - Add automatic conversion of int[] arrays - Substitute Python C-API calls for Python3 with proper replacements that should be used for Python3 - Let functions returning void return Py_None in Python2/Python3 interface - Add Python3 unit tests for soft-constraints callback and utils - Add wrapper for char *[], const char **, and const char *[] function arguments - Replace Python C-API calls to 'PyEval_CallObject' with 'PyObject_CallObject' | 14 November 2016, 17:35:23 UTC |
| 84db4dc | Ronny Lorenz | 14 November 2016, 10:27:48 UTC | Add unstructured domain feature example to RNAfold manpage | 14 November 2016, 10:27:48 UTC |
| cace77d | Ronny Lorenz | 13 November 2016, 12:28:24 UTC | Fix unit test for reverse basepair type array in vrna_md_t data structure | 13 November 2016, 12:28:24 UTC |
| 22df6ec | Ronny Lorenz | 12 November 2016, 11:04:22 UTC | Extend coverage of generic hard constraints for partition function computations | 13 November 2016, 12:21:59 UTC |
| 148b96a | Ronny Lorenz | 13 November 2016, 11:18:06 UTC | Fix bug in model.c resulting in incomplete init of reverse-basepair type array | 13 November 2016, 11:18:06 UTC |
| 2c06d3f | Ronny Lorenz | 10 November 2016, 20:07:25 UTC | Always scale secondary structure such that it fits into EPS bounding box - This also centers the secondary structure plot | 10 November 2016, 20:10:58 UTC |
| 56e38d5 | Ronny Lorenz | 09 November 2016, 15:15:08 UTC | Fix non-TTY-color output for vrna_message_info() | 09 November 2016, 15:15:08 UTC |
| dd4b7dd | Ronny Lorenz | 08 November 2016, 23:58:18 UTC | Merge branch 'dev_permutations' into 'development' Add algorithm to enumerate necklaces with fixed content - Add an implementation of Joe Sawada's 2003 algorithm 'A fast algorithm to generate necklaces with fixed content'. This commit also adds SWIG wrappers for the algorithm. See merge request !61 | 08 November 2016, 23:58:18 UTC |
| 0bc7133 | Ronny Lorenz | 07 November 2016, 18:59:26 UTC | Add algorithm to enumerate necklaces with fixed content - Add an implementation of Joe Sawada's 2003 algorithm 'A fast algorithm to generate necklaces with fixed content'. This commit also adds SWIG wrappers for the algorithm. | 08 November 2016, 23:49:28 UTC |
| 72342e9 | Ronny Lorenz | 03 November 2016, 20:21:25 UTC | Fix compilation for Windows with mingw | 03 November 2016, 20:21:25 UTC |
| 8e99136 | Ronny Lorenz | 02 November 2016, 17:03:09 UTC | Add description on unstructured domains in command files for reference manual | 02 November 2016, 17:03:09 UTC |
| baf56d4 | Ronny Lorenz | 01 November 2016, 20:00:02 UTC | Merge tag 'v2.3.0' into development This is version 2.3.0 | 01 November 2016, 20:00:02 UTC |
| 61b4c41 | Ronny Lorenz | 01 November 2016, 17:04:18 UTC | Bump to version 2.3.0 | 01 November 2016, 17:04:18 UTC |
| d7076ee | Ronny Lorenz | 01 November 2016, 12:09:51 UTC | Implement alternative method for unstructured domain probability computations - The unstructured domain feature introduces two problems regarding the computation of motif probabilities. The default recursions we've implemented now work best whenever the input sequence contains only a few binding sites. However, when there are many binding sites, the current method is extremely slow since for each binding site, any structure motif that contains it must be generated. This commit adds first attempts towards an alternative implementation that first generates all structrure motifs, and only then searches for motif/binding sites within them. Thus it has fewer overhead compared to the default recursions. | 01 November 2016, 12:12:21 UTC |
| 1751f29 | Ronny Lorenz | 01 November 2016, 11:27:03 UTC | Use new EPS dot-plot function in RNAfold | 01 November 2016, 12:12:21 UTC |
| 50ea28f | Ronny Lorenz | 27 October 2016, 08:16:03 UTC | Add new EPS dot-plot function to support auxiliary data | 01 November 2016, 12:12:21 UTC |
| 753bd8c | Ronny Lorenz | 01 November 2016, 12:06:19 UTC | Skip some computations in unstructured domain probability recursions | 01 November 2016, 12:12:21 UTC |
| a88ddfe | Ronny Lorenz | 01 November 2016, 11:24:33 UTC | Make default unstructured domains callbacks more efficient | 01 November 2016, 11:34:18 UTC |
| 03ea7a1 | Ronny Lorenz | 25 October 2016, 16:39:45 UTC | Some code cleanup | 01 November 2016, 11:19:32 UTC |
| 726ea83 | Ronny Lorenz | 25 October 2016, 16:39:08 UTC | Fix unstructured domain handling in multibranch loops | 01 November 2016, 11:19:20 UTC |
| 43104a2 | Ronny Lorenz | 24 October 2016, 09:49:47 UTC | Fail on creating vrna_fold_compound for too long sequences - This fixes a bug in our executables that allowed very long sequences and then failed with segmentation fault upon preparation of recursions. | 24 October 2016, 09:49:47 UTC |
| a826db1 | Ronny Lorenz | 21 October 2016, 10:10:44 UTC | Added new example programs and snippets to reference manual | 21 October 2016, 10:10:44 UTC |
| dc8c51f | Ronny Lorenz | 20 October 2016, 15:45:51 UTC | Finalize SWIG wrapper for unstructured domain feature - Wrap all features to Perl5 and Python2/3 - Simplify and rename some functions in unstructured domains API | 20 October 2016, 15:45:51 UTC |
| 73952f7 | Ronny Lorenz | 20 October 2016, 11:23:49 UTC | Fix concurrent access to global symbol base_pair in API 3.0 functions - This commit fixes a race condition in vrna_mfe() and vrna_mfe_dimer() where after backtracking the MFE structure, each function would re-set the same global base_pair symbol due to backward compatibility issues. Now, wrapper functions that translate the old API to new API 3.0 calls handle setting of this global symbol, since they are not expected to be thread-safe anyway. This should make vrna_mfe(), vrna_mfe_dimer() and related functions thread-safe again. | 20 October 2016, 11:23:49 UTC |
| 1954900 | Ronny Lorenz | 20 October 2016, 10:16:23 UTC | Merge branch 'development' of krios.tbi.univie.ac.at:rna/viennarna into development | 20 October 2016, 10:16:23 UTC |
| 8833a1d | Ronny Lorenz | 16 October 2016, 20:20:12 UTC | Add lots of documentation for SWIG wrapped functions | 16 October 2016, 20:20:12 UTC |
| c39ceb7 | Ronny Lorenz | 16 October 2016, 17:20:40 UTC | Many changes for SWIG interface and rename of VRNA_VC_TYPE_* to VRNA_FC_TYPE_* - Added SWIG interface to manage command files - Remapped vrna_fc_type_e enumeration - Added first functions from file_formats_msa.c - Added findpath.i | 16 October 2016, 17:26:40 UTC |
| 7b09e73 | Ronny Lorenz | 16 October 2016, 15:07:37 UTC | copy callback-ud.i from Python to Python3 | 16 October 2016, 15:07:37 UTC |
| 5670907 | Ronny Lorenz | 15 October 2016, 19:33:49 UTC | Unify how motifs are dertected in dot-bracket structrues - Detect motifs in constraints_ligands.c and unstructured_domains.c - Use detections in RNAfold to annotate MFE, centroid, and MEA structure | 16 October 2016, 15:07:27 UTC |
| d4c0944 | Ronny Lorenz | 15 October 2016, 18:06:03 UTC | Add function to compute pscore for alignments - This also introduces SWIG wrappers for several alignment related functions | 15 October 2016, 18:06:03 UTC |
| 92e3973 | Ronny Lorenz | 13 October 2016, 12:27:26 UTC | Merge branch 'dev_md_copy' into 'development' Add function to copy/clone a set of model settings See merge request !59 | 13 October 2016, 12:27:26 UTC |
| fd82e20 | Ronny Lorenz | 13 October 2016, 12:14:20 UTC | Merge branch 'development' of krios.tbi.univie.ac.at:rna/viennarna into development | 13 October 2016, 12:14:20 UTC |
| 00502b4 | Ronny Lorenz | 13 October 2016, 12:14:00 UTC | Removed git submodules | 13 October 2016, 12:14:00 UTC |
| 125216f | Ronny Lorenz | 13 October 2016, 08:53:53 UTC | Merge branch 'dev_docu_update' into 'development' Some update to reference manual documentation - Mainly typos See merge request !60 | 13 October 2016, 08:53:53 UTC |
| e2ab8cb | Ronny Lorenz | 12 October 2016, 15:37:38 UTC | Include helper files in src/bin in the distribution tarball | 12 October 2016, 15:37:38 UTC |
| d852877 | Ronny Lorenz | 12 October 2016, 15:17:43 UTC | Merge commit '8d38dea17d2fd5e67207a2653f2a15caf084a241' as 'src/Kinfold' | 12 October 2016, 15:17:43 UTC |
| 8d38dea | Ronny Lorenz | 12 October 2016, 15:17:43 UTC | Squashed 'src/Kinfold/' content from commit a0b7e0d git-subtree-dir: src/Kinfold git-subtree-split: a0b7e0d50e6540da22657ca633b5b3a50e5e7e0f | 12 October 2016, 15:17:43 UTC |
| b7bf5f2 | Ronny Lorenz | 12 October 2016, 15:16:40 UTC | Merge commit 'd591078abd7e977cdb25652723e45c47c19908ff' as 'src/RNAforester' | 12 October 2016, 15:16:40 UTC |
| d591078 | Ronny Lorenz | 12 October 2016, 15:16:40 UTC | Squashed 'src/RNAforester/' content from commit 27994dc git-subtree-dir: src/RNAforester git-subtree-split: 27994dc42fc070e1195624ad4ec2ed974e4590a2 | 12 October 2016, 15:16:40 UTC |
| 5e8a435 | Ronny Lorenz | 12 October 2016, 15:16:11 UTC | Merge commit '8ca1b1255e6062ce7438c0b78870c094ec62667c' as 'src/Kinwalker' | 12 October 2016, 15:16:11 UTC |
| 8ca1b12 | Ronny Lorenz | 12 October 2016, 15:16:11 UTC | Squashed 'src/Kinwalker/' content from commit 293b820 git-subtree-dir: src/Kinwalker git-subtree-split: 293b820ddbf631b6ecbb7b2648026e509f45e916 | 12 October 2016, 15:16:11 UTC |
| 60e65ad | Ronny Lorenz | 12 October 2016, 15:14:34 UTC | Remove remaining git submodules - They will be added again using git-subtree | 12 October 2016, 15:14:34 UTC |
| 7305ed9 | Ronny Lorenz | 12 October 2016, 15:09:36 UTC | Merge commit '6e033d481153218060b32052f5fb05527ded71da' as 'interfaces/Perl/RNA' | 12 October 2016, 15:09:36 UTC |
| 6e033d4 | Ronny Lorenz | 12 October 2016, 15:09:36 UTC | Squashed 'interfaces/Perl/RNA/' content from commit 6328bbe git-subtree-dir: interfaces/Perl/RNA git-subtree-split: 6328bbe884e783950380a5f3bbed66140401d98d | 12 October 2016, 15:09:36 UTC |
| 361b81b | Ronny Lorenz | 12 October 2016, 15:04:57 UTC | Removed interfaces/Perl/RNA submodule | 12 October 2016, 15:04:57 UTC |
| 3ceb4f0 | mmann | 11 October 2016, 14:42:19 UTC | Some update to reference manual documentation - Mainly typos | 12 October 2016, 11:38:11 UTC |
| 57407ee | Ronny Lorenz | 12 October 2016, 10:59:24 UTC | Remove unnecessary calls to update vrna_md_t | 12 October 2016, 11:24:57 UTC |
| 12dffd6 | Ronny Lorenz | 11 October 2016, 20:12:17 UTC | Revert C++ style in-place copy for vrna_md_t to something C-like - Now, vrna_md_copy() returns a pointer to the target model. This actually allows this function to create a new model in memory and pass the corresponding address to the outside. | 12 October 2016, 11:24:38 UTC |
| 09d2842 | mmann | 11 October 2016, 14:11:04 UTC | + vrna_md_copy : copies a given parameter model * vrna_md_set_default : uses vrna_md_copy | 12 October 2016, 11:23:32 UTC |
| c4d0baa | Ronny Lorenz | 11 October 2016, 13:34:57 UTC | Fix ML decomposition for circfold - Fixed discrepancy between unique- and non-unique ML decomposition | 11 October 2016, 13:34:57 UTC |
| 7667f33 | Ronny Lorenz | 07 October 2016, 13:05:44 UTC | Add fold_compound methods for subopt and zuker-style subopt to SWIG interfaces - This also restores the old API zukersubopt function | 07 October 2016, 13:05:44 UTC |
| d160125 | Ronny Lorenz | 07 October 2016, 13:02:07 UTC | Fix energy unit in return values and restore backward compatibility for zuker-style subopt | 07 October 2016, 13:03:55 UTC |
| fc1d5f3 | Ronny Lorenz | 03 October 2016, 22:11:32 UTC | Fix Python 2/3 SWIG wrappers for generic soft constraints - Apparently, Py_None is not necessarily NULL - Add first actual unit tests for soft constraint callbacks | 03 October 2016, 22:11:32 UTC |
| a031482 | Ronny Lorenz | 03 October 2016, 22:07:10 UTC | Add useful functions - vrna_db_to_element_string() to annotate each nucleotide according to the loop it resides in - vrna_plist_append() to append one plist to another | 03 October 2016, 22:07:10 UTC |
| e87ed9d | Ronny Lorenz | 03 October 2016, 22:04:44 UTC | Fix dirname/basename functions for windows | 03 October 2016, 22:04:44 UTC |
| 0bdb173 | Ronny Lorenz | 03 October 2016, 07:11:30 UTC | Add utility functions that deal with conversion between units | 03 October 2016, 07:27:21 UTC |
| 5424fc8 | Ronny Lorenz | 01 October 2016, 18:25:49 UTC | Merge branch 'dev_ud_outside' into 'development' Equilibrium Probabilities for unstructured domains See merge request !57 | 01 October 2016, 18:25:49 UTC |
| e47554c | Ronny Lorenz | 01 October 2016, 18:03:33 UTC | Annotate unstructured domain motif probabilities as blueish triangles in dot-plots | 01 October 2016, 18:20:17 UTC |
| e36a7f9 | Ronny Lorenz | 01 October 2016, 14:05:56 UTC | Fixed outside partition function for unstructured domain motifs in multiloops - The only thing that remains implemented for unstructured domain probabilities are generic (soft) constraints | 01 October 2016, 14:50:13 UTC |
| 94739b9 | Ronny Lorenz | 28 September 2016, 10:16:54 UTC | Fix q_ij and qm_ij computation in part_func.c with unstructured domains - Unstructured domains are ALWAYS additional states | 28 September 2016, 16:13:25 UTC |
| bbd7145 | Ronny Lorenz | 27 September 2016, 18:45:33 UTC | Rename VRNA_UNSTRUCTURED_DOMAINS_ML_LOOP to VRNA_UNSTRUCTURED_DOMAINS_MB_LOOP | 27 September 2016, 18:45:33 UTC |
| b6c4cae | Ronny Lorenz | 25 September 2016, 18:03:23 UTC | Exit RNAfold on empty solutions when constraints read from command file | 27 September 2016, 18:07:00 UTC |
| 90ad058 | Ronny Lorenz | 23 September 2016, 16:09:22 UTC | New (more efficient) way to compute outside partition functions for unstructured domain motifs | 27 September 2016, 18:07:00 UTC |
| 18ac7ff | Ronny Lorenz | 23 September 2016, 16:08:06 UTC | Always treat structures with bound unstructured domain motif as separate state! | 27 September 2016, 18:07:00 UTC |
| fca2c7a | Ronny Lorenz | 23 September 2016, 16:04:23 UTC | Add function to retrieve unstructured domain motif sizes for specific sequence positions | 27 September 2016, 18:07:00 UTC |
| d0810b3 | Ronny Lorenz | 17 September 2016, 10:28:03 UTC | Next steps towards outside partition function for unstructured domains | 27 September 2016, 18:07:00 UTC |
| 8577c11 | Ronny Lorenz | 13 September 2016, 17:43:46 UTC | Fix unstructured domain outside contributions for interior loops | 27 September 2016, 18:07:00 UTC |
| efd698e | Ronny Lorenz | 13 September 2016, 15:52:50 UTC | Add contributions for unstructured domains within hairpin loops to outside part | 27 September 2016, 18:07:00 UTC |
| 6ec42a6 | Ronny Lorenz | 12 September 2016, 19:24:45 UTC | Start adding outside partition function for unstructured domains feature | 27 September 2016, 18:07:00 UTC |
| de0c13f | Ronny Lorenz | 27 September 2016, 16:10:08 UTC | Add relevant SWIG wrappers to allow for full soft-constraints control in MFE predictions - This enables one to write funny generic hard constraints such as 'Revert MFE prediction to Maximum Matching' | 27 September 2016, 18:03:10 UTC |
| 8aa202a | Ronny Lorenz | 23 September 2016, 10:31:13 UTC | Fix memory allocation in RNAfold when -o option is used for output file prefix | 23 September 2016, 10:31:13 UTC |
| b48b4ec | Ronny Lorenz | 21 September 2016, 11:49:27 UTC | Fix bug in doc/Makefile.am that prevents HTML installation due to long argument list | 21 September 2016, 11:49:27 UTC |
| d0c840b | Ronny Lorenz | 20 September 2016, 13:31:14 UTC | Add separate source file for file-utilities | 20 September 2016, 13:31:14 UTC |
| d24f6db | Ronny Lorenz | 17 September 2016, 12:06:46 UTC | Silence automake output for SWIG interfaces | 20 September 2016, 13:30:15 UTC |
| bf3dc39 | Ronny Lorenz | 17 September 2016, 12:05:49 UTC | Check for successful linking against libperl at configure time | 17 September 2016, 12:05:49 UTC |
| 719e4eb | Ronny Lorenz | 17 September 2016, 10:14:30 UTC | Require C99 conform compiler - We need C99 macros SIZE_MAX and va_copy for string helper functions vrna_strdup_printf and vrna_strcat_printf | 17 September 2016, 10:14:30 UTC |
| 0e62bbd | Ronny Lorenz | 15 September 2016, 17:24:53 UTC | Add vrna_strcat_printf() function to safely append a formatted string to another string | 15 September 2016, 17:24:53 UTC |
| 23ddb19 | Ronny Lorenz | 15 September 2016, 10:46:35 UTC | Add command parser for unstructured domains | 15 September 2016, 10:46:35 UTC |
| fbec892 | Ronny Lorenz | 15 September 2016, 10:43:52 UTC | Fix backtracking for exterior- and multibranch loops with unstructured domains | 15 September 2016, 10:46:21 UTC |
| ffd10fa | Ronny Lorenz | 12 September 2016, 15:08:58 UTC | Cleanup in mfe.c and part_func.c - Mostly removal of unused variables | 12 September 2016, 15:48:55 UTC |
| 39b3166 | Ronny Lorenz | 12 September 2016, 14:33:06 UTC | Some changes in warning messages of RNAfold | 12 September 2016, 14:33:06 UTC |
| ce1d0c5 | Ronny Lorenz | 12 September 2016, 14:32:47 UTC | Add commands file support to RNAcofold | 12 September 2016, 14:32:47 UTC |
| 3545a7a | Ronny Lorenz | 12 September 2016, 14:30:37 UTC | Fix non-canonical interior loops and circular interior loops with soft constraints | 12 September 2016, 14:30:37 UTC |
| 362e913 | Ronny Lorenz | 12 September 2016, 06:31:39 UTC | Unify how executable programs parse commandline parameters and apply corresponding settings | 12 September 2016, 12:20:32 UTC |
| 9308b60 | Ronny Lorenz | 12 September 2016, 12:17:12 UTC | Removed vrna_file_constraints_read() in favor for vrna_file_commands_read() - The files formerly known as constraints definition files are termed command files now. The format we implement here is to allow for specification of not only structure constraints (hard/soft) but also ligand motifs (via soft constraints feature), unstructured domain motifs, and structured domains (in the future) | 12 September 2016, 12:17:12 UTC |
| 3db255e | Ronny Lorenz | 12 September 2016, 10:52:55 UTC | Enable soft constraints in command files | 12 September 2016, 10:52:55 UTC |
| 980d543 | Ronny Lorenz | 09 September 2016, 20:22:07 UTC | Add separate page for SWIG wrapper notes | 09 September 2016, 20:26:01 UTC |
| 29e1891 | Ronny Lorenz | 09 September 2016, 11:28:07 UTC | Add new soft constraints functions to SWIG wrappers - This also updates the documentation for how to use these functions through the scripting language interface | 09 September 2016, 11:28:07 UTC |
| 0920e58 | Ronny Lorenz | 09 September 2016, 09:20:18 UTC | Replace vrna_sc_add_* functions with actually adding ones and rename vrna_sc_add_* to vrna_sc_set_* | 09 September 2016, 09:22:43 UTC |
| 48d0a40 | Ronny Lorenz | 08 September 2016, 17:28:45 UTC | Add soft constraints functions to 'really' add energies for unpaired, and paired positions - The previous set of functions required a vector, and a matrix with energy values for unpaired, and paired positions, respectively. The new set of functions now allows one to set single positions individually. Furthermore, the old implementation always deleted previously applied soft constraints. The new functions really add soft constraints instead. | 08 September 2016, 17:28:45 UTC |
| 1c4a5ac | Ronny Lorenz | 08 September 2016, 10:50:15 UTC | Add ID manipulation feature to RNAeval and enable colorized output | 08 September 2016, 10:50:15 UTC |
| e35736c | Ronny Lorenz | 08 September 2016, 10:49:36 UTC | Minor comment change in RNAcofold.c | 08 September 2016, 10:49:36 UTC |
| 5df60ce | Ronny Lorenz | 07 September 2016, 16:55:56 UTC | Do not duplicate message string for vrna_message_* functions - Otherwise, it might be that an 'out of memory' message won't be displayed | 07 September 2016, 16:55:56 UTC |
| 030e47a | Ronny Lorenz | 07 September 2016, 16:24:21 UTC | Rename error/warning/info message functions - The previously existing functions vrna_message_error() and vrna_message_warning() are variadic functions now. As is vrna_message_info(). This is the least invasive way since it should be completely backward compatible. Their complementary functions that take a va_list as argument are named vrna_message_verror(), vrna_message_vwarning(), and vrna_message_vinfo(). - All the above functions have a description in the reference manual | 07 September 2016, 16:24:21 UTC |
| b1328c7 | Ronny Lorenz | 07 September 2016, 15:26:38 UTC | Use error/warning/info message functions wherever possible | 07 September 2016, 15:26:38 UTC |
| f8256c4 | Ronny Lorenz | 07 September 2016, 13:31:23 UTC | Replace calls to get_line() with vrna_read_line() in file_formats_msa.c | 07 September 2016, 13:31:48 UTC |
| e6b3d98 | Ronny Lorenz | 07 September 2016, 13:24:29 UTC | Added variatic functions for error/warning/info messages | 07 September 2016, 13:24:29 UTC |
